In the past few years, the area of comparative genomics of malaria parasites has begun to come of age, with the completion of genome sequencing projects of four Plasmodium species, and several functional genomics studies. A picture is emerging of a parasite genome that is highly adapted to its mammalian and vector hosts, and which uses post-transcriptional gene-silencing as one method for the control of gene expression. The genome is compartmentalized into a core of conserved housekeeping genes, sandwiched between subtelomerically located genes encoding surface antigens. Species-specific gene families shape the preference of the parasite for host cells, in addition to determining interactions with the host immune-system. Recent research has led to the description of a motif that is conserved across Plasmodium species and which plays a central role in protein export into the host cell.